[English] 日本語
Yorodumi
- PDB-1e5p: Crystal structure of aphrodisin, a sex pheromone from female hamster -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e5p
TitleCrystal structure of aphrodisin, a sex pheromone from female hamster
ComponentsAPHRODISIN
KeywordsLIPOCALIN / PHEROMONE / HAMSTER
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMESOCRICETUS AURATUS (golden hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsVincent, F. / Brown, K. / Spinelli, S. / Cambillau, C. / Tegoni, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of aphrodisin, a sex pheromone from female hamster.
Authors: Vincent, F. / Lobel, D. / Brown, K. / Spinelli, S. / Grote, P. / Breer, H. / Cambillau, C. / Tegoni, M.
History
DepositionJul 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / reflns / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APHRODISIN
B: APHRODISIN
C: APHRODISIN
D: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)69,5564
Polymers69,5564
Non-polymers00
Water12,665703
1
A: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.050, 48.920, 123.547
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99583, -0.03603, 0.08386), (0.00504, 0.93907, 0.34368), (-0.09113, -0.34182, 0.93534)-2.18702, 10.94148, -14.25162
2given(-0.98626, 0.16046, 0.03936), (0.16233, 0.89681, 0.41155), (0.03074, 0.41229, -0.91053)-51.32672, -11.73474, 70.58553
3given(-0.99779, 0.03586, -0.05595), (0.03319, 0.9983, 0.04786), (0.05757, 0.04589, -0.99729)-43.31905, 22.33536, 61.29768

-
Components

#1: Protein
APHRODISIN


Mass: 17389.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MESOCRICETUS AURATUS (golden hamster) / Gene: MESOCRICETUS AURATUS APHRODISIN GENE / Organ: VAGIN / Plasmid: PQE31 / Cellular location (production host): CYTOPLASM
Gene (production host): MESOCRICETUS AURATUS APHRODISIN GENE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834DE3 / References: UniProt: P09465
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: APHRODISIN, SECRETED IN HAMSTER VAGINAL DISCHARGE, IT FUNCTIONS AS AN APHRODISIAC ...FUNCTION: APHRODISIN, SECRETED IN HAMSTER VAGINAL DISCHARGE, IT FUNCTIONS AS AN APHRODISIAC PHEROMONE, RELIABLY ELICITING COPULATORY BEHAVIOR FROM MALE HAMSTER. SIMILARITY: BELONGS TO THE LIPOCALIN FAMILY.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 %
Crystal growMethod: vapor diffusion / pH: 3.8
Details: PEG 8K 28%, 150MM AS, 10MM NACL PH 3.8, [P]=2.65MG/NL
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Method: vapor diffusion / pH: 3.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128 %PEG80001reservoir
2150 mMammonium sulfate1reservoir
3100 mMsodium citrate1reservoirpH3.8
42.65 mg/mlprotein1drop
52.5 M1dropNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978, 0.9795, 0.9324, 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 1999 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97951
30.93241
40.9331
ReflectionResolution: 1.6→30 Å / Num. obs: 89441 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 23.77 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.31 / % possible all: 94
Reflection
*PLUS
Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Rmerge(I) obs: 0.31

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: 1A3Y

1a3y


Resolution: 1.63→15 Å / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.098
Details: SEVERAL RESIDUES ARE IN ALTERNATE CONFORMATION, AND ARE PRECEEDED BY A AND B LIKE AMET, BMET. THE PROTEIN USED TO SOLVE THE STRUCTURE HAS BEEN SELENIATED SO THE METHIONINES IN THE PDB FILE ...Details: SEVERAL RESIDUES ARE IN ALTERNATE CONFORMATION, AND ARE PRECEEDED BY A AND B LIKE AMET, BMET. THE PROTEIN USED TO SOLVE THE STRUCTURE HAS BEEN SELENIATED SO THE METHIONINES IN THE PDB FILE ARE SELENOMETHIONIES (MSE) SOME OCCUPANCIES HAVE BEEN SET TO 0 OR LESS THAN 1 BECAUSE OF LACK OF DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2202 2.5 %RANDOM
Rwork0.194 ---
obs0.194 88875 96 %-
Refinement stepCycle: LAST / Resolution: 1.63→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 0 703 5456
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8292
X-RAY DIFFRACTIONp_mcangle_it2.5352.5
X-RAY DIFFRACTIONp_scbond_it2.8533
X-RAY DIFFRACTIONp_scangle_it3.964.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1220.3
X-RAY DIFFRACTIONp_planar_tor3.92
X-RAY DIFFRACTIONp_staggered_tor15.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more